Over the last several decades, modern society has collectively placed the environment in an incredibly fragile state. Years of fossil fuel burning, mass deforestation, and disposal of waste into oceans have all contributed to rising temperatures, loss of biodiversity, and extreme weather trends [1-3]. Perhaps the most visible sign of this impact stems from plastic, which plays an ever-increasing role in climate change, as we have grown closely reliant on it in the 70 years since its invention. While light, durable, and cheap to produce, plastics originate from fossil fuels and greatly contribute to greenhouse gasses [4]. They are also creeping into sediment on ocean floors, remaining as artifacts for centuries into the future [5]. If we focus on eliminating plastic waste from our oceans and lands, do we have a chance to slow down its harmful impact? Despite the mess we have made, is it possible that nature has already started adapting to these new conditions?
There are countless documentaries on streaming platforms focused on the impact humans have had on earth, including that of plastic use specifically. In spite of this exposure, we continue to produce 300 million tons of plastic each year, with an estimated 14 million tons ending up in the oceans alone [6]. While the full extent of plastic’s impact on the environment may not be understood, experts such as Carrol Muffett, a legal scholar and the head of the Center for International Environment Law, are confident that “the plastics crisis is a climate crisis hiding in plain sight” [7].
This crisis began in the 20th century when large-scale plastic production became popular in the 1950s. Plastics are formed through chains of molecules called ethylene and propylene, which are commonly found in fossils [8]. Due to their inability to biodegrade, these materials have been steadily accumulating in landfills, oceans, and terrestrial habitats. It is currently estimated that plastic bottles need roughly 450 years to decompose, and plastic straws take 200 years[9]. With current technology, permanently removing plastic involves a destructive thermal treatment like combustion, or burning the plastic, which releases toxins such as heavy metals into the air. These metals accelerate climate change and put the health of local communities at greater risk [10].
Plastic has become so common in terrestrial and marine spheres that it has been proposed as a key geological marker of the unit of time called the Anthropocene—anthropo- for “human” and -cene for “era” of geological time. It is now commonly accepted that today’s geological period is defined by human activities affecting all earth system processes. Plastics already dispersed in sedimentary deposits, which allow for temporal resolution within the Anthropocene, are known as “techno fossils” preserved in layers of rock called strata [11]. Thus, plastics are not only contributing to the wave of pollutants ravaging the environment, but they have also significantly modulated recent geological layers, leaving their mark on the earth from within.
To slow down the rate at which plastic is deposited in lands and oceans, solutions are needed for its safe removal. In fact, some scientists have observed that certain species in the environment have adapted to their dire new circumstances by solving this problem themselves. Indeed, populations of bacteria living amongst plastics in landfills have shown promising signs of being able to break down plastics into smaller molecules [12]. Using these bacteria as inspiration, an opportunity has arisen to look at the myriad adaptations of the natural world and make use of them on a larger scale.
Many of the most recent and exciting inventions in biotechnology have been adapted from systems that are naturally occurring in other organisms. For example, the CRISPR-Cas9 system was first discovered in the bacterial immune response to viral infection and has quickly led to numerous applications in gene editing across biomedical research. The Nobel laureate Frances Arnold recognized early on that nature was “the best bioengineer in history” [13]. Known for her contributions to the field of bioengineering, she revolutionized the use of directed evolution to create new enzymes for various applications. For example, the creation of enzymes optimized for the purpose of biofuel production has recently been industrialized [14].
An example of the process of directed evolution. Mutations can be induced in genes through processes such as polymerase chain reaction (PCR). Mutated gene libraries are cloned into bacteria like E. coli to assess gene function in the context of a specific desired phenotype. Cells that gain a survival advantage are isolated to investigate which gene mutation gave them this advantage. Source: https://commons.wikimedia.org/wiki/File:DE_cycle.png.
There are generally two approaches to enzyme engineering: directed evolution and rational design. Whereas rational design requires a comprehensive understanding of a protein’s structure, directed evolution does not require such preexisting knowledge. Instead, directed evolution guides proteins like enzymes towards a functional goal by mimicking natural selection, where a change in a given enzyme may yield improved survival of a bacterium compared to organisms without this change. These changes can be achieved by sequential mutagenesis, a repeated process of inducing random genetic mutations in the host’s DNA and screening whether the efficacy of a desired enzyme’s function has improved.
With this principle, we can take any enzyme that already exists and modify it in a controlled setting to achieve an optimal function of interest. In the case of plastic waste removal, we can look at enzymes of plastic-eating bacteria in the wild, study their baseline rate of plastic digestion, and use directed evolution to improve the efficiency of this metric.
This theory is being put into practice by multiple groups studying plastic-eating bacteria. These microbes were first discovered at a Japanese landfill more than five years ago. A group of Japanese scientists showed that a specific species of bacteria (Ideonella sakaiensis) could break down one of the most widely distributed types of plastics, polyethylene terephthalate (PET/polyester), through the use of two enzymes called PET hydrolase and MHETase. These early studies showed that bacteria in these landfills had evolved to digest 60mg of this plastic in roughly six weeks [15]. This finding supported the notion that bacteria can adapt very quickly, especially when their nutrient intake is limited, given that these PET enzymes have not been found in any other organisms. However, initial reports also showed that highly crystallized PET, abundant in plastic bottles, took longer to digest, suggesting that further modifications to these naturally occurring enzymes would be needed for their use in widespread plastic cleanup.
Building off of the discoveries in Japanese landfills, the French company Corbios sponsored research into a modified enzyme that was able to degrade PET bottles in under ten hours but only at 70˚C (158˚F) [16]. British researchers improved on this work by developing a version of the enzyme that can effectively work at room temperature by combining the two enzymes involved in the naturally occurring bacterial digestion, guided by an understanding of their structure [17].
Visual of plastic-eating bacteria found in landfills near water bottles and their processing of the PET. Image is from a French source. Plastic PET composition is shown at the top. The first enzyme PETase converts PET to MHET, which gets further broken down by the enzyme MHETase into the monomers ethylene glycol and terephthalic acid. The description under the monomers suggests that these products are used for growth by the bacteria. Source: https://commons.wikimedia.org/wiki/File:Ideonella_sakaiensis_PTEase.svg.
Previous approaches to engineering enzymes to digest plastic have relied primarily on rational design, but directed evolution could yield a longer list of enzyme candidates for this purpose. However, methods for high-throughput screening of this specific test case have been largely lacking until recently. A pre-print (not yet peer reviewed) published at the end of 2021 by a team from the University of Manchester was the first report of an automated capacity for testing directed evolution on enzymes capable of degrading plastic polymers [18]. Through iterative random mutagenesis, the team was able to create an enzyme they named HotPETase which can degrade the material found in commercial bottles and laminated materials quicker than previous models. If these results are published and replicated, it may not be long before trials involving mass production of this enzyme could be used to combat the ever-growing crisis of plastic waste.
Our reliance on the abundance and convenience of plastic has been a major contributor to both climate change and environmental and geological disruption. Finding a safe route for plastic disposal requires new thinking and new technologies. Advancements in protein engineering alongside the discovery of naturally evolved plastic-digesting enzymes in bacteria shed light on an exciting avenue for what the future may hold in our ability to reduce plastic waste. Large-scale use of such enzymes will require additional research and regulation to avoid negative effects on other organisms in the natural world, and any further evolution beyond our own direction will require careful monitoring. Nevertheless, looking to nature for signs of adaptation is instructive and revelatory. If the current era is defined by the problems humans have made, perhaps the next will reflect the solutions other life has provided.
Edited by Nick Bulthuis
References
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12. Migdon, Brooke. “New Study Shows Microbes Are Evolving to Eat Plastic.” The Hill, 14 Dec. 2021, https://thehill.com/changing-america/sustainability/environment/585802-new-study-shows-microbes-are-evolving-to-eat. Accessed 11 Feb. 2022.
13. “The Nobel Prize: Women Who Changed Science: Frances H. Arnold.” The Official Website of the Nobel Prize - NobelPrize.org, https://www.nobelprize.org/womenwhochangedscience/stories/frances-arnold. Accessed 11 Feb. 2022.
14. Woo, Marcus Y. “Researcher Tries Directed Evolution to Craft Better Biofuels – Climate Change: Vital Signs of the Planet.” NASA, NASA, 26 Nov. 2018, https://climate.nasa.gov/news/659/researcher-tries-directed-evolution-to-craft-better-biofuels/. Accessed 11 Feb. 2022.
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